Posts by Mayte Suarez-Farinas

...
Hi Laurent.
I gave up on this for a while, but will try again.
I got a new computer , all new installation from scratch and still I get an error when i try to publish a KEGG result.
keggParams<-new("KEGGHyperGParams", geneIds = DEGi_entrez, universeGeneIds=UnivEntrez,
...

... Dear All,
I am successfully using the ReportingTools package to detect over-
expressed categories
using hypergeometric Test for Gene Ontologies and PFAM follwoing the
package vignette.
When I tried to do the same using KEGG pathways, the function publish
does not work.
I am surprise because class P ...

... Dear annotation builders
I notice that one of my favorite genes DEFB4A is missing from the
hgu133plus2.db
the NetAffy database says that probeset 207356_at correspond to gene
DEFB4A
yet getSYMBOL('207356_at','hgu133plus2.db') returns NA. This happen in
newer versions of
this package, since it has b ...

... I tried all your advice: reinstall R, change mirror, still
biocLite("affycoretools") does not install the package bit
automatically
and downloading the tgz from bit, the package bit does not compile
Mayte Suarez-Farinas
Research Assistant Professor
Laboratory of Investigative Dermatology
Biostatist ...

... Hi James and Dan
I installed R from scratch and then run the following two lines:
biocLite() (success)
biocLite("affycoretools")
which, after installing several packages gave me the "error: package
AnnotationDbi could not be loaded" (see ALL outputs below)'
Dan, here is the output of biocin ...

...
Dear James, Henrik and Steve
I tried biocLite("ff") and got the msg: package ?ff? is not available
(for R version 3.0.1)
(see below). Then I went ahead and download the tar package form
(http://cran.r-project.org/web/packages/ff/index.html) and used R CMD
install to install it. However,
while load ...

... I updated to the most recent R version. After this brand new
installation, I get the following error while loading library
affycoretools:
library(affycoretools)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()),
versionCheck = vI[[j]]) :
there is no package called ff
Error: packag ...

... Dear All,
I am trying to use the easyRNASeq package with 6 RNAseq samples from
mouse.
Single end, unstranded protocol, 50bp reads. I followed the vignettes
and wrote this short code:
library("easyRNASeq")
library(Rsamtools)
library(DESeq)
library(edgeR)
library(GenomicRanges)
library(parallel)
lib ...